4-160870229-G-C

Position:

• chr4-160870229-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.331 in 151,964 control chromosomes in the GnomAD database, including 11,418 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (11418 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.160870229G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50241 AN: 151846 Hom.: 11386 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.322

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.331 AC: 50328 AN: 151964 Hom.: 11418 Cov.: 32 AF XY: 0.321 AC XY: 23862 AN XY: 74256

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.323

Alfa AF: 0.105 Hom.: 141

Bravo AF: 0.354

Asia WGS AF: 0.222 AC: 770 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.5
DANN	Benign	0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6811083; hg19: chr4-161791381;